Genomic ancestry in urban Afro-Brazilians

Brazil is the result of interethnic crosses of European, African and Amerindian populations. Allelic frequencies for seven STR loci (TH01, TPOx, CSF1PO, vWA, FES/FPS, F13A1 and CD4), obtained from a sample of 70 individuals identified as Afro-Brazilian and 150 as mulatto, are presented here. Based on the frequencies of these genetic markers, estimates of interethnic admixture showed 62%, 26% and 12% of European, African and Amerindian contribution, respectively, for the mulatto sample and 37% and 63% of European and African contribution, respectively, for the Afro-Brazilian sample.     

Population structure and admixture in Cerro Largo, Uruguay, based on blood markers and mitochondrial DNA polymorphisms.

Recent studies of the Uruguayan population revealed different amounts of Amerindian and African genetic contributions. Our previous analysis of Afro-Uruguayans from the capital city of the Department of Cerro Largo showed a high proportion of African genes, and the effects of directional mating involving Amerindian women. In this paper, we extended the analysis to a sample of more than 100 individuals representing a random sample of the population of the whole Department. Based on 18 autosomal markers and one X-linked marker, we estimated 82% European, 8% Amerindian, and 10% African contributions to their ancestry, while from seven mitochondrial DNA site-specific polymorphic markers and sequences of hypervariable segment I, we determined 49% European, 30% Amerindian, and 21% African maternal contributions. Directional matings between Amerindian women and European men were detected, but differences involving Africans were not significant. Data about the specific origins of maternal lineages were also provided, and placed in a historical context.     

Estimates of interethnic admixture in the Brazilian population using a panel of 24 X‐linked insertion/deletion markers

Objectives. In this study, we aimed to identify ancestry informative haplotypes and make interethnic admixture estimates using X‐chromosome markers. Methods. A significant sample (461 individuals) of European, African, and Native American populations was analyzed, and four linkage groups were identified. The data obtained were used to describe the ancestral contribution of populations from four different geographical regions of Brazil (745 individuals). Results. The global interethnic admixture estimates of the four mixed populations under investigation were calculated applying all the 24 insertion/deletion (INDEL) markers. In the North region, a larger Native Americans ancestry was observed (42%). The Northeast and Southeast regions had smaller Native American contribution (27% in both of them). In the South region, there was a large European contribution (46%). Conclusions. The estimates obtained are compatible with expectations for a colonization model with biased admixture between European men (one X chromosome) and Native American and African women (two X chromosomes), so the 24 X‐INDEL panel described here can be a useful to make admixture interethnic estimates in Brazilian populations. Am. J. Hum. Biol., 2010. © 2010 Wiley‐Liss, Inc.     

Admixture estimates for the population of Havana City

Background: The Cuban population is essentially a result of the admixture between Spanish, West African and, to a lesser degree, Amerindian tribes that inhabited the island.

Aim: The study analysed the genetic structure of the three principal ethnic groups from Havana City, and the contribution of parental populations to its genetic pool.

Subjects and methods: According to genealogical information and anthropological traits, 206 subjects were classified as Mulatto, of Spanish decent or of African descent. Seventeen Ancestry Informative Markers, with high difference in frequency between parental populations, were selected to estimate individual and group admixture proportions. The statistical analyses were performed using the ADMIX, ADMIX95 and STRUCTURE 2.1 packages.

Results: The results demonstrate a high level of European and African admixture in Mulattos (57–59% European; 41–43% West African). The European contribution was higher in those of Spanish descent (85%) while in those of African descent, the West African contribution ranged between 74% and 76%. Genetic structure was only detected in Mulattos and those of African descent. An Amerindian contribution was not detectable in the studied sample.

Conclusion: Our findings indicate the existence of admixture and genetic structure in the population of Havana City. This study represents one of the first steps towards understanding Cuban population admixture in order to produce successful experimental designs for admixture mapping.     

Genomic ancestry of a sample population from the state of São Paulo,Brazil

Allelic frequencies of eight autosomal short‐tandem repeat (STR) loci (TH01, TPOx, CSF1PO, vWA, FES/FPS, F13A1, F13B, and CD4) were determined in 400 individuals born in the State of São Paulo. No significant deviations from Hardy‐Weinberg equilibrium were found in any loci analyzed. The Unweighted Pair‐Group Method with Arithmetic Mean (UPGMA) tree constructed based on genetic distances revealed that the present population was grouped with Europeans, and separated from African and Amerindian populations. Estimates of admixture components based on the gene identity method revealed 79% European, 14% African, and 7% Amerindian contributions to this Brazilian population sample. Am. J. Hum. Biol. 18:702–705, 2006. © 2006 Wiley‐Liss, Inc.     

Amerindian ancestry in Argentina is associated with increased risk for systemic lupus erythematosus

Previous studies have demonstrated that in admixed populations, West African ancestry is associated with an increased prevalence of systemic lupus erythematosus (SLE). In the current study, the effect of Amerindian ancestry in SLE was examined in an admixed population in Argentina. The Argentine population is predominantly European with approximately 20% Amerindian admixture, and a very small (<2%) contribution from West Africa. The results indicate that Amerindian admixture in this population is associated with a substantial increase in SLE susceptibility risk (Odds Ratio=7.94, P=0.00006). This difference was not due to known demographic factors, including site of collection, age and gender. In addition, there were trends towards significance for Amerindian ancestry influencing renal disease, age of onset and anti-SSA antibodies. These studies suggest that populations with Amerindian admixture, like those with West African admixture, should be considered in future studies to identify additional allelic variants that predispose to SLE.     

Impact of population admixture on the distribution of immune response co-stimulatory genes polymorphisms in a Brazilian population

Co-stimulatory molecules are essential in the orchestration of immune response and polymorphisms in their genes are associated with various diseases. However, in the case of variable allele frequencies among continental populations, this variation can lead to biases in genetic studies conducted in admixed populations such as those from Brazil. The aim of this study was to evaluate the influence of genomic ancestry on distributions of co-stimulatory genes polymorphisms in an admixed Brazilian population. A total of 273 individuals from the north of Brazil participated in this study. Nine single nucleotide polymorphisms in 7 genes (CD28, CTLA4, ICOS, CD86, CD40, CD40L and BLYS) were determined by polymerase chain reaction-restriction fragment length polymorphism. We also investigated 48 insertion/deletion ancestry markers to characterize individual African, European and Amerindian ancestry proportions in the samples. The analysis showed that the main contribution was European (43.9%) but also a significant contribution of African (31.6%) and Amerindian (24.5%) ancestry. ICOS, CD40L and CD86 polymorphisms were associated with genomic ancestry. However there were no significant differences in the proportions of ancestry for the other SNPs and haplotypes studied. Our findings reinforce the need to apply AIMs in genetic association studies involving these polymorphisms in the Brazilian population.     

Assessing individual interethnic admixture and population substructure using a 48–insertion‐deletion (INSEL) ancestry‐informative marker (AIM) panel

Estimating the proportions of different ancestries in admixed populations is very important in population genetics studies, and it is particularly important for detecting population substructure effects in case‐control association studies. In this work, a set of 48 ancestry‐informative insertion‐deletion polymorphisms (INDELs) were selected with the goal of efficiently measuring the proportions of three different ancestries (sub‐Saharan African, European, and Native American) in mixed populations. All selected markers can be easily analyzed via multiplex PCR and detected with standard capillary electrophoresis. A total of 593 unrelated individuals representative of European, African, and Native American parental populations were typed, as were 380 individuals from three Brazilian populations with known admixture patterns. As expected, the interethnic admixture estimates show that individuals from southern Brazil present an almost exclusively European ancestry; Afro‐descendant communities in the Amazon region, apart from the major African contribution, present some degree of admixture with Europeans and Native Americans; and a sample from Belém, in the northeastern Amazon, shows a significant contribution of the three ethnic groups, although with a greater European proportion. In summary, a panel of ancestry‐informative INDELs was optimized and proven to be a valuable tool for estimating individual and global ancestry proportions in admixed populations. The ability to accurately infer interethnic admixtures highlights the usefulness of this marker set for assessing population substructure in association studies, particularly those conducted in Brazilian and other Latin American populations sharing trihybrid ancestry patterns. Hum Mutat 31:184–190, 2010. © 2009 Wiley‐Liss, Inc.     

Dissimilarities in the process of formation of curiaú, a semi‐isolated Afro‐Brazilian population of the Amazon region

The genetic consequences of the social policy of the past in relation to the formation of Afro‐Brazilian societies are interesting and have been studied at various biological levels (classical polymorphisms and the mitochondrial and nuclear levels. These allow the estimation of the contribution of African genes and the participation of other ethnic groups in the formation of these communities. With this objective, uniparental systems of exclusively maternal (mtDNA) or paternal (Y‐DNA) inheritance in the Curiaú community were analyzed. The results demonstrate a differential contribution of the maternal and paternal genetic systems. Thirty‐three sequences were identified by mtDNA analysis; 53% showing an African and 47% an Amerindian origin. For the paternal system, 57% were of African, 37% of European, and 6% of Amerindian origin. Am. J. Hum. Biol. 14:440–447, 2002. © 2002 Wiley‐Liss, Inc.     

Strong Amerindian Mitonuclear Discordance in Puerto Rican Genomes Suggests Amerindian Mitochondrial Benefit

A large discrepancy between the Amerindian contribution to the mitochondrial and nuclear genetic components of 55 Puerto Rican (PR) genomes from the 1000 Genomes Project is identified, with Amerindian mitochondrial haplotypes being highly represented (67.3%), in strong contrast to the Amerindian autosomal contribution (12.9%). I examine the potential causes behind this strong mitonuclear discordance. The Amerindian contribution to the X chromosome is 19.8%, implying assortative mating with Amerindian females during the establishment of the PR population. However, this scenario does not account for the extraordinarily high Amerindian mitochondrial contribution. Demographic simulation of simple assortative mating scenarios during establishment of the PR population indicates that the observed Amerindian mitochondrial contribution is higher than expected. The simulations show that expansion from a small founding population does not produce the observed frequencies, instead producing the frequencies expected under neutrality, with the Amerindian mitochondrial frequencies approximately twice the Amerindian autosomal proportion. In addition, multiple replicated simulations show that drift is an unlikely explanation for the elevated Amerindian mitochondrial frequency, as these are unable to produce the elevated Amerindian mitochondrial frequency observed in the PR genomic dataset, under a range of different starting conditions. I conclude that the mitonuclear discordance appears most consistent with adaptive mitochondrial benefit; however, the molecular mechanism(s) remain to be characterized before this can be confirmed and warrant further investigation. Lastly, I show potential evidence of selection on autosomes and allosomes, using admixture proportions. Interestingly, the major histocompatibility complex locus on chromosome 6 shows greatly elevated single nucleotide polymorphism density but is unaccompanied by strong admixture variance. The observations on mitonuclear discordance may affect the interpretation of apparent assortative mating in recent human admixture events, which should be treated with caution when relying only on mitochondrial haplotype frequencies.     

Use of short tandem repeats loci to study the genetic structure of several populations from Zulia State, Venezuela.

Genetic relationships between populations can be studied by comparing genotypic and allelic similarities. This investigation aims to demonstrate that selected autosomal microsatellite markers could be used to study the genetic structures of different populations living in northwest Venezuela, in Zulia State. Seven autosomal systems (CSF1PO, TPOX, TH01, vWA, D7S820, D13S317, and D5S818) were tested by PCR in a multiplex format on 688 different chromosomes from unrelated individuals living in Maracaibo, "Isla de Toas," and "San José de Heras," and from two Amerindian populations from the "Sierra de Perijá," Barí' and Yukpa. Allele frequencies, Hardy-Weinberg equilibria, genetic distances, phylogenetic trees, and ethnic admixtures were estimated. The study shows the existence of a clear genetic difference among these populations in accordance with their historic evolution. The populations of Maracaibo and "Isla de Toas" showed a triracial origin, with a large European contribution, followed by an Amerindian component and a small African component. The indigenous groups, Barí' and Yukpa, showed exclusively an Amerindian component, and "San José de Heras" showed only an African component. These results indicate that microsatellite markers are useful for molecular anthropology in a regional and worldwide context and provide important genetic information about contemporary populations of Venezuela.     

HLA genes in Barranquilla (North Colombia): Searching for cryptic Amerindian genes

America First Inhabitants population (Amerindians, Na Dene and Eskimos) underwent a drastic population reduction and gene exchange after Europeans and Africans arrival after 1492 AD. Barranquilla population may be a good model to study present day population admixture in South America. HLA-A, -B and -DRB1 DNA typing has been performed in 188 unrelated individuals originated in the area and speak Spanish language; they showed apparent European/African and mixed characters. HLA genetic European/African features were found and only 1.85% Amerindian one. This contrasts with neighboring Cuban population where 10% HLA Amerindian characters appear.     

Genetic composition of Brazilian population samples based on a set of twenty‐eight ancestry informative SNPs

Ancestry informative SNPs can be useful to estimate individual and population biogeographical ancestry. Brazilian population is characterized by a genetic background of three parental populations (European, African, and Brazilian Native Amerindians) with a wide degree and diverse patterns of admixture. In this work we analyzed the information content of 28 ancestry‐informative SNPs into multiplexed panels using three parental population sources (African, Amerindian, and European) to infer the genetic admixture in an urban sample of the five Brazilian geopolitical regions. The SNPs assigned apart the parental populations from each other and thus can be applied for ancestry estimation in a three hybrid admixed population. Data was used to infer genetic ancestry in Brazilians with an admixture model. Pairwise estimates of F_st among the five Brazilian geopolitical regions suggested little genetic differentiation only between the South and the remaining regions. Estimates of ancestry results are consistent with the heterogeneous genetic profile of Brazilian population, with a major contribution of European ancestry (0.771) followed by African (0.143) and Amerindian contributions (0.085). The described multiplexed SNP panels can be useful tool for bioanthropological studies but it can be mainly valuable to control for spurious results in genetic association studies in admixed populations. Am. J. Hum. Biol., 2010. © 2009 Wiley‐Liss, Inc.     

Prevalence of dopamine and 5HT2C receptor polymorphisms in Amerindians and in an urban population from Argentina.

We report on the frequency of DRD2A1, DRD3A1, DRD4/2R-10R, and 5HT2CA1 variants in the population of the city of La Plata (Argentina) and in Amerindians from Argentina, Paraguay, and Chile. In the Amerindian sample, the prevalence of DRD2A1 and DRD4/4R variants were, respectively, significantly lower and significantly higher than frequencies reported in other Native Americans. Comparison of average allele and genotype frequencies between La Plata and Amerindians showed significant differences for 5HT2CA1 and DRD4. As La Plata is a population with predominant European and Amerindian components, we used mtDNA and Y-specific markers to subdivide the La Plata sample into two strata: Amerindian La Plata and non-Amerindian La Plata. Significant variations between the two strata were detected for DRD2A1, DRD3A1, and DRD4/4R allele frequencies, and for the homozygous DRD4/4R/4R genotype. Several controversial reports suggest a possible association between a variant of DRD and/or 5HT2C receptor genes and the clinical expression of several psychiatric disorders. We suggest that ethnic variations in the prevalence of the allelic forms of these genes may be a confounding factor to be taken into consideration in studies of association between dopaminergic and serotonergic receptor genotypes and neuropsychiatric and mood disorders.     

Genetic relationship of the Guambino, Paez, and Ingano Amerindians of southwest Colombia using major histocompatibility complex class II haplotypes and blood groups.

We analyzed the Amerindian tribes, Guambiano, Ingano, and Paez of the southwest section of Colombia by major histocompatibility complex class II typing and blood group analysis in order to establish their genetic relationship. In addition, genetic admixture with Caucasian and African ancestry were determined based on blood group typing. The Paez showed admixture with Caucasian populations (22.4%), while the Ingano and Guambiano showed some admixture with Black populations (9.2 and 4.6%, respectively). The Ingano had MHC class II haplotypes found mainly in Amerindian and Asian populations with no evidence of class II haplotypes of African origin. MHC class II haplotypes of Amerindian and Asian populations and some haplotypes frequently found in European Caucasians and Asians and haplotypes of European Caucasians were found in Guambiano and Paez tribes. We compared our results with those previously reported for four Amerindian tribes on Northern Colombia. The presence of some MHC class II haplotypes in the Guambiano, Paez, and Ingano tribes and their absence in the Chibcha speaking groups of Northern Colombia suggest that these tribes originated, together with other Amerindians, from a separate migration or by genetic drift from an ancestral population. Therefore they are genetically distant from Chibcha speaking tribes of Colombia.     

Admixture estimates for Churuguara, a Venezuelan town in the State of Falcón

BACKGROUND: The present Venezuelan population is the admixture product of Amerindians, Europeans and Africans, a process which was not homogeneous over the country. Blood groups, STRs and VNTRs, specifically D1S80, have been used successfully in admixture studies, but few have been made in Venezuela. AIM: This study aims to estimate the admixture components of Churuguara, Venezuela, and to evaluate the genetic relationship of this population with other Venezuelan as well as worldwide populations through principal component analysis and the study of dendrograms based on genetic distances. SUBJECTS AND METHODS: Gene frequencies of blood groups ABO and Rh (only anti D), of STRs VWA, F13A01, FES/FPS and VNTR D1S80 were studied in a sample of 60 individuals born in Churuguara, a Venezuelan town of admixed ancestry in the State of Falc6n. Admixture was estimated with Chakraborty's gene identity method, and Nei's standard genetic distance was used to build two dendrograms with the neighbour-joining approach, one based on the three STRs and the other based only on D1S80. Principal component analyses with the gene frequencies of these markers were also performed. RESULTS: The frequency of allele ABO*O was 0.788, of ABO*A was 0.187 and of RH*D was 0.74. D1S80 showed 16 different alleles with a heterozygosity of 0.880, whilst the three STRs showed only eight different alleles and heterozygosities between 0.733 and 0.797. The estimates of admixture obtained in this analysis were 52.5% for the Spanish parental group, 27.6% for the African and 19.9% for the Amerindian. Comparison of Churuguara with other Latin American populations shows that its African component is not as high as that observed in Colombian Choco, but it is higher than that observed in other samples from Colombia, Chile and Maracaibo (Venezuela). CONCLUSIONS: Results of the admixture analysis are consistent with those obtained with two dendrograms and principal component analyses, suggesting that the strong initial Amerindian component of 500 years ago has been diluted by the continuous flow of European genes, mainly Spanish, to this region.     

HLA class I polymorphism in the Cuban population

The extreme polymorphism found at some of the human leukocyte antigen (HLA) system loci makes it an invaluable tool for population genetic analyses. In the present study the genetic polymorphism of the Cuban population was estimated at HLA-A, -B, and -Cw loci by DNA typing. HLA class I allele and haplotype diversity were determined in 390 unrelated Cuban individuals (188 whites and 202 mulattos) from all over the country. In whites 19, 27, and 14 allele families for the HLA-A, -B, and -Cw loci, respectively, were identified. In mulattos, for the same loci, 20, 18, and 14 allele families were identified. Allele and haplotypes frequencies, comparisons with other worldwide populations based on genetic distances, neighbor-joining dendrograms, and correspondence analyses were estimated. Most of the identified allele groups and haplotypes are also common to sub-Saharan African and Europeans populations. However, Amerindian and Asian alleles were also detected at lower frequencies. The results clearly reveal the high diversity and interethnic admixture of the studied population. Our results provide useful information for the further studies of the Cuban population evolution and disease association in terms of HLA class I genes.     

Frequency of twinning in two Costa Rican ethnic groups: An update

Variation in the frequency of twinning among human populations has been presumed to reflect genetic differences. It has been commonly reported that populations of African ancestry have the highest, those of Asian ancestry the lowest, and those of European and Middle‐Eastern ancestry intermediate frequencies of twinning. Populations from the Americas have been reported to have intermediate twinning frequencies, presumably reflecting their admixture. In this context, Madrigal (1994. Am J Hum Biol 6:215–218) reported virtually identical (and high) twinning frequencies in two Costa Rican ethnic groups, one of African, the other of Euro‐Amerindian ancestry. These frequencies were interpreted in light of frequent inter‐ethnic unions, and it was predicted that the two groups would not differ substantially in gene frequencies of several blood enzyme systems. This paper reports the gene frequencies of both groups for such systems. The samples differ significantly for systems that have clearly different frequencies in African and European populations. Given that the groups are actually different in gene frequencies and not homogenous as predicted earlier, the conclusion that twinning frequencies are similar as a result of a similar genetic make up can be questioned. The results challenge the assumption that if populations have similar twinning frequencies it is because they are genetically similar and argue for a stronger environmental component for twinning frequencies. Am. J. Hum. Biol. 13:220–226, 2001. © 2001 Wiley‐Liss, Inc.     

Gene Admixture in the Costa Rican Population

The general population of Costa Rica has sometimes been considered to be the product of an amalgamation of groups of diverse origin. To determine the magnitude of accumulated admixture since Spanish colonization, 11 classic genetic markers were analyzed in a total of 2196 individuals originating from five distinct regions of the country. A maximum likelihood approach was used. The proportions of genes of European, Amerindian and African ancestry were found to be 61%, 30% and 9% of the total population, respectively. Variation was observed at a regional level, with an increased European influence in the North (66%) and Central (65%) regions. Meanwhile an increase in Amerindian ancestry was found in the South (38%), and a higher incidence in the contribution of African genes was detected in the coastal regions (13% in the Atlantic and 14% in the North Pacific). A principal component (PC) analysis showed that 76% of the existing variability can be explained by the first two PCs, which is in agreement with the variations observed in the admixture process by geographic area. It has been concluded that the Costa Rican population is truly trihybrid, similar to populations in other Latin American countries; however, it differs from them fundamentally by the proportion of gene flow from ancestral populations.     

African-derived South American populations: A history of symmetrical and asymmetrical matings according to sex revealed by bi- and uni-parental genetic markers

Estimates of African, European, and Amerindian contributions to the gene pool of 11 predominantly African-derived South American populations were obtained using five autosomal and one Y chromosome hypervariable loci, as well as mitochondrial DNA (sequences of the first hypervariable segment of the control region, plus two restriction sites and the presence or absence of the CoII/tRNA^Lys intergenic 9-bp deletion). The three latter characteristics are reported here for the first time for 42 individuals living in three Brazilian populations. Thirty-eight sequences were identified in these persons; 17 (45%) could be classified as being of African, 4 (11%) of Amerindian, and 2 (5%) of European origin. Evidence for asymmetrical matings in relation to sex and ethnic group was obtained for nine of the 11 populations. The most consistent finding was the introduction of European genes through males, but the results differ in the several communities, indicating the importance of local factors in such interactions. Am. J. Hum. Biol. 11:551–563, 1999. © 1999 Wiley-Liss, Inc.